Giacomo Baruzzo, PhD

Giacomo Baruzzo got a Bachelor Degree in Information Engineering at University of Padova in 2011. He got a Master Degree in Computer Engineering (2013, Advisor Prof. Gianfranco Bilardi; final mark: 110/110) and a Ph.D. in Information Engineering (2017, Advisor Prof. Barbara Di Camillo) at University of Padova, working on genome assembly and sequence alignment topics. From 2017 to 2021, he was a postdoctoral researcher at the Department of Information Engineering, University of Padova, working on computational methods for mining biological data coming from high-throughput sequencing technologies.
From January 2022, he is a researcher (RTDa) at the Department of Information Engineering, University of Padova, and he works in the SysBioBig lab (System Biology and Bioinformatics Group) with Prof. Barbara Di Camillo.
His current research is aimed at developing efficient algorithms, methods and software for the preprocessing, analysis and interpretation of biological data from high-throughput sequencing technologies, especially single cell RNA-Sequencing, bulk RNA-Sequencing and 16S rDNA-Sequencing.

PhD in Information Engineering at the University of Padova, Padova, Italy

Jan 2014 - Dec 2016
Thesis title: Improving the RNA-Seq analysis pipeline: read alignment and expression level quantification.
Advisor: Prof. Barbara Di Camillo

Master's Degree in Computer Engineering at the University of Padova, Padova, Italy

Oct 2011 - Oct 2013
Thesis title: A maximum likelihood approach to genome assembly.
Advisor: Prof. Gianfranco Bilardi

Bachelor's Degree in Information Engineering at the University of Padova, Padova, Italy

Oct 2008 - Sep 2011

Postdoctoral Researcher (RTDA)
at the Department of Information Engineering, University of Padova, Padova, Italy

Jan 2022 - Present
Research project: "Environmental Antimicrobial Resistance Load Tackling via Intelligent Systems (EARLIeSt)". Funding: REACT EU – PON “Ricerca e Innovazione 2014-2020” - DM 1062/2021

Senior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Nov 2020 - Dec 2021
Research project: "Development of single cell RNA-seq bioinformatics methods and tools to study cell-cell communication and spatio-temporal evolution of multi-cells systems".

Junior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Oct 2017 - Oct 2020
Research project: DEI PROACTIVE 2017 - "From Single-Cell to Multi-Cells Information Systems Analysis"

Visiting Postdoctoral Researcher
at Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia

Mar 2019 - Apr 2019
Research project: 1° Session of the Italian–Slovenian Joint Commission on Scientific and Technological Cooperation: "Computational and data visualization approaches to mining of large-scale data in single-cell genomics".

Junior Postdoctoral Researcher
at the Department of Information Engineering, University of Padova, Padova, Italy

Jan 2017 - Sep 2017
Research project: BIOBIG - “Analisi di Big Data in Bioinformatica”

Visiting PhD Student
at ITMAT Bioinformatics Group, Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, USA.

Jun 2015 - Dec 2015

"Best performing teams (3rd place)" at "Metagenomics Diagnosis for Inflammatory Bowel Disease Challenge (MEDIC)", sbv IMPROVER Computational Challenge series 2019-2020

Team GiGi, University of Padova, Italy: Barbara Di Camillo, Marco Cappellato, Mehdi Poursheikhali Asghari, Sebastian Daberdaku, Giacomo Baruzzo, Filippo Pietrobon, Ilaria Patuzzi.

Travel Fellowship at 19th Annual Meeting of the Bioinformatics Italian Society (BITS) 2023

Best talk award at 8th Mediterranean School of Complex Networks (MSCX 2023), 25-30 June 2023, Catania, Italy.

Talk title: Bioinformatics for complex biological systems: unraveling cell-cell and bacterial interactions

G. Baruzzo and K. Hayer, E. Ji Kim, B. Di Camillo, G. Fitzgerald, G. Grant,
“Simulation-based comprehensive benchmarking of RNA-seq aligners”,
Nature Methods, 2016, 14(2):135–139. (DOI: 10.1038/nmeth.4106)

A. Dal Molin, G. Baruzzo, B. Di Camillo,
“Single-cell RNA-sequencing: assessment of differential expression analysis methods”,
Frontiers in Genetics, 2017, 8:62. (DOI: 10.3389/fgene.2017.00062)

F. Sambo, F. Finotello, E. Lavezzo, G. Baruzzo, G. Masi, E. Peta, M. Falda, S. Toppo, L. Barzon, B. Di Camillo,
“Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene”,
BMC Bioinformatics, 2018, 19(1):343. (DOI: 10.1186/s12859-018-2360-6)

G. Baruzzo, I. Patuzzi, B. Di Camillo,
“SPARSim single cell: a count data simulator for scRNA-seq data”,
Bioinformatics, 2019, 36(5): 1468-1475. (DOI: 10.1093/bioinformatics/btz752)

I. Patuzzi, G. Baruzzo, C. Losasso, A. Ricci, B. Di Camillo,
“metaSPARSim: a 16S rRNA gene sequencing count data simulator”,
BMC Bioinformatics, 2019, 20(9): 1-13. (DOI: 10.1186/s12859-019-2882-6)

G. Baruzzo and I. Patuzzi, B. Di Camillo,
“Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results”,
BMC Bioinformatics, 2021, 22(15). (DOI: 10.1186/s12859-022-04587-0)

G. Baruzzo, G. Cesaro, B. Di Camillo,
“Identify, quantify and characterize cellular communication from single cell RNA sequencing data with scSeqComm”,
Bioinformatics, 2022, 38(7):1920-1929. (DOI: 10.1093/bioinformatics/btac036)

M. Cappellato, G. Baruzzo, B. Di Camillo,
“Investigating differential abundance methods in microbiome data: a benchmark study”,
PLOS Computational Biology, 2022, 18(9):e1010467. (DOI: 10.1371/journal.pcbi.1010467)

G. Cesaro, M. Milia, G. Baruzzo, G. Finco, F. Morandini, A. Lazzarini, P. Alotto, N.F. da Cunha Carvalho de Miranda, Z. Trajanoski, F. Finotello, B. Di Camillo,
“MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach”,
Bioinformatics Advances, 2022, 2(1). (DOI: 10.1093/bioadv/vbac092)

The complete list of publications is avaiable here link to CV.

Number of peer-reviewed journals articles: 20 (19 research articles, 1 commentary article)

Number of conference contributions: 50 (24 abstract+poster, 6 abstract+poster+oral, 15 abstract+oral, 5 short-article +oral)

Number of journal article citations:

including self-citations: 464 (Scopus) - 417 (WoS) - 830 (Google Scholar)
excluding self-citations: 452 (Scopus) - 405 (WoS) - 818 (Google Scholar)

h-index: 9 (Scopus) - 9 (Web of Science) - 11 (Google Scholar)

Scopus ID: 57192312589

WoS ID: AAE-5962-2022

ORCID: 0000-0001-6129-5007

Google Scholar ID: hSVdrbwAAAAJ

The complete list of articles and conference contributions is avaiable here link to CV.

Institute of Electrical and Electronics Engineers - IEEE (role: member)

Association for Computing Machinery - ACM (role: member)

International Society of Computational Biology - ISCB (role: member)

Bioinformatics Italian Society - BITS (role: associate member)

Young-InfoLife group, InfoLife National Laboratory of CINI (role: co-founder and co-coordinator)

Publicity co-chair, Proceedings co-chair, Organizing committee, Program committee
at 16th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2019)

Certosa di Pontignano, Siena, Italy, from July 9 to July 11, 2019

Local committee
at 18th Annual Meeting of the Bioinformatics Italian Society (BITS 2022)

Verona, Italy, from June 27 to June 29, 2022

Co-Chair, Co-Chair organizing committee
Workshop “Spatial transcriptomics and cell-cell communication modeling: new opportunities to study the cellular dynamics of biological systems” at New Trends in Bioinformatics by ECCB - 21st European Conference on Computational Biology (ECCB 2022)

Virtual event, September 13, 2022

Co-chair, co-organizer and instructor
Tutorial “Software containerization in bioinformatics: how to make reproducible, portable and reusable bioinformatics software&pipelines” at New Trends in Bioinformatics by ECCB - 21st European Conference on Computational Biology (ECCB 2022)

Sitges, Barcellona, Spain, September 18, 2022

Co-chair, co-organizer and instructor
Tutorial “How to make reproducible, portable and reusable bioinformatics software using software containerization” at 31st Conference on Intelligent Systems for Molecular Biology & 22nd European Conference on Computational Biology (ISMB/ECCB 2023)

Lyon, France, July 23, 2023

Co-chair
at YOUNG BITS, RSG-Italy & CINI Young-InfoLife Symposium at 19th Annual Meeting of the Bioinformatics Italian Society (BITS 2023)

Bari, Italy, from June 21 to June 23, 2023

Program committee, Local committee, Session Chair
at 18th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2023)

Padova, Italy, from September 6 to September 8, 2023

Co-Organizer, Co-Chair
Special Session "An Italian snapshot on present and future informatics research in bioinformatics - CINI Infolife" at 18th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2023)

Padova, Italy, from September 6 to September 8, 2023

Scientific committee
at YOUNG BITS, RSG-Italy & CINI Young-InfoLife Symposium at 20th Annual Meeting of the Bioinformatics Italian Society (BITS 2024)

Trento, Italy, from June 12 to June 16, 2024

Co-Organizer
Special Session "Informatics research in bioinformatics: contributions from the CINI-InfoLife network" at 19th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2024)

Benevento, Italy, from September 4 to September 6, 2024

Program committee
at 19th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2024)

Benevento, Italy, from September 4 to September 6, 2024

Co-Organizer, Scientific committee
Young Minds at Work: Blending Biochemistry and Bioinformatics - 2nd Edition

Virtual event, from December 10 to December 12, 2024

Journal referee: IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Journal of Biomedical and Health Informatics, Lecture Notes in Bioinformatics, BMC Bioinformatics, BMC Genomics, Bioinformatics, Briefings In Bioinformatics, Bioinformatics Advances, PLOS Computational Biology, Journal of Biomedical Informatics, Computational and Structural Biotechnology Journal, Frontiers in Bioinformatics, NAR Genomics and Bioinformatics

Conference referee: Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2024, MODIMO Workshop on Multi-Omics Data Integration for Modelling Biological Systems (within ACM International Conference on Information and Knowledge Management (CIKM) 2023), Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2023, Research in Computational Molecular Biology (RECOMB) 2022, IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2021, Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2021, Research in Computational Molecular Biology (RECOMB) 2021, Research in Computational Molecular Biology (RECOMB) 2020

Proceedings editor: Proceedings of the 16th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology

Editor: Springer Lecture Notes in Bioinformatics (LNBI). Proceedings of the 18th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2023), Padova, Italy, from September 6 to September 8, 2023.

Editor: BMC Bioinformatics. Special issue dedicated to the 18th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2023).

Editor: BMC Medical Informatics and Decision Making. Special issue dedicated to the 18th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2023).

Invited seminar: "Working with RNA sequencing data: challenges and strategies for data analysis" at ITMAT Bioinformatics, Institute for Translational Medicine and Therapeutics, University of Pennsylvania

Philadelphia, USA, May 3, 2018

Conference oral presentation: "SPARSim: taking account of data sparsity in single cell and 16S rRNA gene sequencing" at 15th Annual Meeting of the Bioinformatics Italian Society (BITS)

Turin, Italy, June 28, 2018

Conference oral presentation: "SPARSim Single Cell: a count data simulator for single cell RNA-seq data" at 3rd Annual MAQC Society Conference

Riva del Garda, Italy, April 9, 2019

Conference oral presentation: "Reliable simulation of count data for single cell RNA sequencing" at Network Tools and Applications for Biology (NETTAB) and Bioinformatics and Computational Biology Conference (BBCC) 2019 Meeting

Fisciano, Italy, November 13, 2019

Conference oral presentation: "Zero-imputation in 16S rRNA gene studies: do we need it?" at Bioinformatics and Computational Biology Conference (BBCC) 2020 Meeting

Virtual conference, November 18, 2020

Conference oral presentation: "scSeqComm: a bioinformatic tool to identify, quantify and characterize cellular communication from single cell RNA sequencing data" at 18th Annual Meeting of the Bioinformatics Italian Society (BITS)

Virtual conference, July 2, 2021

Conference oral presentation: "Analyze cellular communication from single cell RNA sequencing data with scSeqComm" at Bioinformatics and Computational Biology Conference (BBCC) 2021 Meeting

Virtual conference, December 2, 2021

Invited talk: "Data standardisation and sharing - A lesson from bioinformatics" at Cognition and Natural Sensory Processing Workshop 2022 (CNSP 2022)

Virtual conference, July 20, 2022

Oral presentation: "Bioinformatics for complex biological systems: unraveling cell-cell and bacterial interactions" at 8th Mediterranean School of Complex Networks (MSCX 2023)

Catania, Italy, June 26, 2023

Conference oral presentation: "Comprehensive benchmarking of differential abundance methods in microbiome data" at 31st Conference on Intelligent Systems for Molecular Biology & 22nd European Conference on Computational Biology (ISMB/ECCB 2023)

Lyon, France, July 25, 2023

Conference oral presentation: "scSeqComm: a statistical and network-based framework to infer inter- and intra-cellular communication from single-cell RNA sequencing data" at 31st Conference on Intelligent Systems for Molecular Biology & 22nd European Conference on Computational Biology (ISMB/ECCB 2023)

Lyon, France, July 24, 2023

Conference oral presentation: "Comprehensive benchmarking of network inference methods for 16S rDNA-Seq data" 19th Conference on Computational Intelligence Methods for Bioinformatics & Biostatistics (CIBB 2024)

Benevento, Italy, September 4, 2024

2023-2024: Lecturer (with responsibility of the course) at “Scientific Computing and Object Oriented Programming” [ING-INF/05] (48 hours, 6 CFU - responsible for 4 CFU)

Master Degree course of Mathematical Engineering (A.Y. 2023/2024) - Department of Civil, Environmental and Architectural Engineering, University of Padova, Padova, Italy

2023-2024: Lecturer (with responsibility of the course) at “Computational Genomics” [INF/01 and ING-INF/06] (48 hours, 6 CFU)

Master Degree course of Bioengineering (A.Y. 2023/2024) - Department of Information Engineering, University of Padova, Padova, Italy

2023-2024: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXIX series - Department of Information Engineering, University of Padova, Padova, Italy

2022-2023: Lecturer (with responsibility of the course) at “Scientific Computing and Object Oriented Programming” [ING-INF/05] (48 hours, 6 CFU)

Master Degree course of Mathematical Engineering (A.Y. 2022/2023) - Department of Civil, Environmental and Architectural Engineering, University of Padova, Padova, Italy

2022-2023: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXVIII series - Department of Information Engineering, University of Padova, Padova, Italy

2021-2022: Lecturer (with responsibility of the course) at “Scientific Computing and Object Oriented Programming” [ING-INF/05] (48 hours, 6 CFU)

Master Degree course of Mathematical Engineering (A.Y. 2021/2022) - Department of Civil, Environmental and Architectural Engineering, University of Padova, Padova, Italy

2021-2022: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXVII series - Department of Information Engineering, University of Padova, Padova, Italy

2021-2022: Teaching assistant at “Elementi di Informatica e Programmazione” [INF/01 and ING-INF/05] (Didattica integrativa, 30 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2021/2022) - Department of Information Engineering, University of Padova, Padova, Italy

2020-2021: Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (20 hours, 5 credits)

PhD Program in Information Engineering, XXXVI series - Department of Information Engineering, University of Padova, Padova, Italy

2020-2021: Teaching assistant at “Elementi di Informatica e Programmazione” [INF/01 and ING-INF/05] (Didattica integrativa, 30 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2020/2021) - Department of Information Engineering, University of Padova, Padova, Italy

2019-2020: Co-Lecturer (with responsibility of the course) at “Advanced topics in scientific and parallel programming with practical application to the CAPRI HPC infrastructure” (10 hours, 2.5 credits)

PhD Program in Information Engineering, XXXV series - Department of Information Engineering, University of Padova, Padova, Italy

2019-2020: Teaching assistant at “Elementi di Informatica e Programmazione” [INF/01 and ING-INF/05] (Didattica integrativa, 40 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2019/2020) - Department of Information Engineering, University of Padova, Padova, Italy

2018-2019: Teaching assistant at “Elementi di Informatica e Programmazione” [INF/01 and ING-INF/05] (Didattica integrativa, 50 hours)

Bachelor Degree course of Biomedical Engineering (A.Y. 2018/2019) - Department of Information Engineering, University of Padova, Padova, Italy

2015-2016: Teaching assistant at “Bioingegneria per la Genomica” [ING-INF/06]

Master Degree course of Bioengineering (A.Y. 2015/2016) - Department of Information Engineering, University of Padova, Padova, Italy

Giacomo Baruzzo has served as supervisor or co-supervisor for 2 PhD student's thesis (PhD Course in Information Engineering), 15 Master Degree students's thesis (Computer Engineering, Bioengineering and Molecular Biology) and 7 Bachelor Degree students's thesis (Information Engineering and Biomedical Engineering) at the University of Padova. He is currently co-supervising 5 PhD students (PhD Course in Information Engineering) at the University of Padova.